Chris,
I too rely heavily on the Berendsen methods for T- and P-coupling, and have
always found them satisfactory. I have not seen much beyond the casual
references to the fact that N-H T-coupling and Parrinello-Rahman P-coupling are
superior in terms of membrane simulations. I have tried both, and have found
both setups to be equally reasonable in their results. It seems, overall, that
Nose-Hoover schemes are often applied using NAMD and CHARMM software. I don't
know if this choice is motivated by the software, or the force fields used.
There are a few casual references to Berendsen being less than optimal in the
literature and in archived presentation materials (which I can probably unearth
if I can recall my Googling :).
Based on experience, I too would agree that Berendsen suffices, and only made
mention of the N-H argument as a talking point, something that others have argued.
If I come across any of these references again, I will be sure to post them to
the list to continue the discussion.
-Justin
[EMAIL PROTECTED] wrote:
Hi Justin,
I wonder if you could expand upon the following statement, or perhaps
offer some links or references.
"Some argument can be made that N-H is more applicable to membrane
simulations."
I am interested because I use a Berendsen thermostat for membrane
simulations. To be entirely honest, I have no particular understanding
of the consequence of this choice beyond the oft-heard statement that
Berendsen T-coupling doesn't yield the correct ensemble. But it is very
intuitive and, as you say, it's usage is quite common and I have thus
far relied on these points to guide my choice of temperature-coupling
algorithm. Therefore I am hoping to take advantage of this opportunity
to learn a bit more about temperature coupling as you seem to understand
it quite well.
I am hoping that you can outline the logic underlying the 'correct
ensemble' statement and indicate how this is especially applicable to
membrane simulations.
I do realize that this is a large request on this type of mailing list.
Please feel free to decline.
Much obliged,
Chris.
-- original message --
I have used the Berendsen method almost exclusively in my simulations,
and it is
widely used in most of the literature I read. While the argument can be
made
that Nose-Hoover gives a result closer to the true ensemble than
Berendsen, I
think both are sufficient for simple protein in water simulations. Some
argument can be made that N-H is more applicable to membrane simulations.
As for whether or not you need to slowly increase the temperature, it is
really
up to you. Usually such rigor is not necessary, as often position
restraints
are applied to the protein during initial equilibration. I have never
experienced any adverse effects of simply setting the initial temperature,
although that's not to say it's not possible :)
Just my $0.02.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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